Cotton fleahopper, Pseudatomoscelis seriatus (Reuter) (Hemiptera: Miridae), is a piercing–sucking pest of cotton (Gossypium hirsutum L.) that feeds preferentially on developing flower buds, called squares. Heavy infestations cause yield reductions that result from abscission of squares damaged by the cotton fleahopper feeding. Antixenosis, or nonpreference, has been reported as a mechanism of host plant resistance in cotton to cotton fleahopper. Square structure, particularly the placement of the reproductive tissues, and stylet penetration were investigated as factors that influence resistance to cotton fleahopper in cotton lines derived from crosses with Pilose, a cultigen of upland cotton resistant to cotton fleahopper, and backcrossed with high-yielding, susceptible lines. Ovary depth varied among the lines tested and was found to be a heritable trait that affected the ability of a fleahopper's feeding stylets to penetrate the reproductive tissues in the square and might influence preference. Behavioral assays suggested antixenosis as a mechanism of host plant resistance, and the trait conferring antixenosis was found to be heritable. Results suggest ovary depth plays a role in conferring resistance to cotton fleahopper and is an exploitable trait in resistance breeding.